Messias, A.; Santos, D. E. S.; Pontes, F. J. S.; Lima, F. S.; Soares, T. A. (2021) The tug of war between Al3+ and Na+ for order-disorder transitions in Lipid-A membranes. Phys. Chem. Chem. Phys., v. 23, p. 15127–15137. DOI:10.1039/D1CP02173G
Wei, G.-W. ; Soares, T. A. ; Wahab, H.A.; Wang, R. (2021) Computational Chemistry in Asia. Journal of Chemical Information and Modeling, v. 61, p. 547-547.
Freire, R. V. M.; Pillco-Valencia, Y.; Da Hora, G. C. A.; Ramstedt, M.; Sandblad, L.; Soares, T. A.; Salentinig, S. (2021) Antimicrobial peptide induced colloidal transformations in bacteria-mimetic vesicles: Combining in silico tools and experimental methods. Journal of Colloid and Interface Science, v. 596, p. 352-363.
DOI: 10.1016/j.jcis.2021.03.060
Maciel, L.; Barbosa, A. S.; De Alencar-Filho, E. B.; Soares, T. A.; Dos Anjos, J. V. (2021) A second generation of 1,2,4-oxadiazole derivatives with enhanced solubility for inhibition of 3-hydroxykynurenine transaminase (HKT) from Aedes aegypti. RSC Medicinal Chemistry, v. 12, p. 222-236.
De Nicola, A.; Soares, T. A.; Santos, D. E. S.; Bore, S. L.; Sevink, G. J. A.; Cascella, M.; Milano, G. (2021) Aggregation of Lipid A Variants: a Hybrid Particle-Field Model. Biochimica et Biophysica Acta. v. 1865, p. 129570.
DOI: 10.1016/j.bbagen.2020.129570
Merz, K. M.; Amaro, R.; Cournia, Z. ; Rarey, M.; Soares, T. A. ; Tropsha, A. ; Wahab, H.A.; Wang, R. (2020) Editorial: Method and Data Sharing and Reproducibility of Scientific Results. Journal of Chemical Information and Modeling, v. 60, p. 5868-5869.
Rusu, V. H.; Santos, D. E. S.; Poleto, M. D.; Galheigo, M. M.; Gomes, A. T. A.; Verli, H.; Soares, T. A.; Lins, R. D. (2020) Rotational Profiler: A Fast, Automated, and Interactive Server to Derive Torsional Dihedral Potentials for Classical Molecular Simulation. Journal of Chemical Information and Modeling. v. 60, p. 5923–5927.
Messias, A.; Santos, D. E. S.; Pontes, F. J. S.; Lima, F. S.; Soares, T. A. (2020) Out of Sight, Out of Mind: The Effect of the Equilibration Protocol on the Structural Ensembles of Charged Glycolipid Bilayers. Molecules. v. 25 (21), p 5120-5136. Invited peer-review contribution to special issue Combined Quantum Mechanical and Molecular Mechanical Methods and Simulations II
DOI: 10.3390/molecules25215120
E. Apra, E.J. Bylaska, W.A. De Jong, N. Govind, K. Kowalski, T.P. Straatsma, M. Valiev, H.J.J. van Dam, Y. Alexeev, J.L. Anchell, V. Anisimov, F. Aquino, R. Atta-Fynn, J. Autschbach, N.P. Bauman, J.C. Becca, D.E. Bernholdt, K. Bhaskaran-Nair, S. Bogatko, P. Borowski, J. Boschen, J. Brabec, A. Bruner, E. Cauet, Y. Chen, G.N. Chuev, C. Cramer, J. Daily, M.J.O. Deegan, T.H. Dunning, M. Dupuis, K.G. Dyall, G. Fann, S.A. Fischer, A. Fonari, H. Fruchtl, L. Gagliardi, J. Garza, N. Gawande, S. Ghosh, K. Glaesemann, A.W. Goetz, J. Hammond, V. Helms, E.D. Hermes, K. Hirao, S. Hirata, M. Jacquelin, L. Jensen, B.G. Johnson, H. Jonsson, R.A. Kendall, M. Klemm, R. Kobayashi, V. Konkov, S. Krishnamoorthy, M. Krishnan, Z. Lin, R.D. Lins, R.J. Littlefield, A.J. Logsdail, K. Lopata, W. Ma, A.V. Marenich, J.M. del Campo, D. Mejia-Rodriguez, J.E. Moore, J.M. Mullin, T. Nakajima, D.R. Nascimento, J.A. Nichols, P.J. Nichols, J. Nieplocha, A. Otero-de-la-Roza, B.J. Palmer, A. Panyala, T. Pirojsirikul, B. Peng, R. Peverati, J. Pittner, L. Pollack, R.M. Richard, P. Sadayappan, G.C. Schatz, W.A. Shelton, D. William Silverstein, D.M. Smith, T.A. Soares, D. Song, M. Swart, H.L. Taylor, G. Thomas, V. Tipparaju, D.G. Truhlar, K. Tsemekman, T. Van Voorhis, A. Vazquez-Mayagoitia, P. Verma, O. Villa, A. Vishnu, K. Vogiatzis, D. Wang, J. Weare, M.J. Williamson, T. Windus, K. Wolinski, A.T. Wong, Q. Wu, C. Yang, Q. Yu, M. Zacharias, Z. Zhang, Y. Zhao, R. Harrison. (2020) NWChem: Past, Present, and Future. J. Chem. Phys. v. 152, p. 184102-184126.
Soares, T.A.; Wahab, H.A. (2020). Outlook on the Development and Application of Molecular Simulations in Latin America. Journal of Chemical Information and Modeling, v. 60, p. 435-438. Editorial for the Special Issue of JCIM on Molecular Simulation in Latin America.
Santos, D. E. S.; Pontes, J. F. S.; Lins, R. D.; Coutinho, K.; Soares, T. A. (2020) SuAVE: A Tool for Analyzing Curvature-Dependent Properties in Chemical Interfaces. Journal of Chemical Information and Modeling, v. 60(2), p. 473-484.
Maciel, L.G.; Dos Anjos, J.V.; Soares, T.A. (2020) Fast and low-cost evaluation of hydroxykynurenine activity. METHODSX, v. 7, p. 100982.
DOI: 10.1016/j.mex.2020.100982
Maciel, L.G.; Oliveira, A.A.; Romão, R.P.; Leal, L.L.L..; Guido, R.V.C.; Silva-Filha, M.H.; dos Anjos, J.V; Soares, T. A. (2020) Discovery of 1,2,4-oxadiazole derivatives as a novel class of noncompetitive inhibitors of 3-hydroxykynurenine transaminase (HKT) from Aedes aegypti. Bioorganic and Medicinal Chemistry v. 28, p. 115252-115265.
Soares, T.A.; Wahab, H.A. (2019). Molecular Simulation in Latin America: Coming of Age. Journal of Chemical Information and Modeling, v. 59, p. 3601-3602. Editorial for the Special Issue of JCIM on Molecular Simulation in Latin America.
Capeletti, L. B.; De Oliveira, J. F. A.; Loiola, L. M. D.; Galdino, F. E.; Santos, D. E. S.; Soares, T. A.; Freitas, R. O.; Cardoso, M. B. (2019) Gram‐Negative Bacteria Targeting Mediated by Carbohydrate–Carbohydrate Interactions Induced by Surface‐Modified Nanoparticles. Advanced Functional Materials, v. 29, p. 1904216.
Yamanaka, T. ; A. De Nicola, A. ; G. Munaò, G. ; Soares, T.A. ; Milano, G. (2019) Effect of the Ligand’s Bulkiness on the Shape of Functionalized Gold Nanoparticles in Aqueous Solutions: A Molecular Dynamics Study. Chem. Phys. Lett, v. 731, p. 136576-136583.
DOI: 10.1016/j.cplett.2019.07.004
Silva, J. Y. R. ; Proenza, Y. G. ; Da Luz, L. L. ; De Sousa Araújo, S. ; Filho, M. A. G. ; Junior, S. A. ; Soares, Thereza A. ; Longo, R. L. (2019) A thermo-responsive adsorbent-heater-thermometer nanomaterial for controlled drug release: (ZIF-8,EuxTby)@AuNP core-shell. Materials Science & Engineering C-Materials for Biological Applications, v. 102, p. 578-588.
DOI: 10.1016/j.msec.2019.04.078
Lima, M. ; Nader, M. ; Santos, D. E. S. ; Soares, T. A. (2019) Compatibility of GROMOS-Derived Atomic Parameters for Lipopolysaccharide Membranes with the SPC/E Water Model and Alternative Long-Range Electrostatic Treatments Using Single Nonbonded Cutoff and Atom-Based Charge Schemes. Journal of the Brazilian Chemical Society, v. 30, p. 2219-2230. Invited peer-review contribution to special issue Brazilian Women in Chemistry
DOI: 10.21577/0103-5053.20190119
Santos, D. E. S. ; Li, D. ; Ramstedt, M. ; Gautrot, J. ; Soares, T. A. (2019) Conformational Dynamics and Responsiveness of Weak and Strong Polyelectrolyte Brushes: Atomistic Simulations of PDMAEMA and PMETAC. Langmuir, v. 35, p. 5037–5049.
DOI: 10.1021/acs.langmuir.8b04268
Silva-Jr., J.J.; Soares, T.A.; Pol-Fachin, L; Machado, D.C.; Rusu, V. H.; Aguiar, J.P.; Rodrigues, C.G. (2019) Alpha-Hemolysin Nanopore Allows Discrimination of the Microcystin Variants. RSC Advances, v. 9, p. 14683-14691.
Oliveira, I. A. ; Pol-Fachin, L. ; de Carvalho, S. T. ; Lins, R. D. ; Soares T. A.; Mohana-Borges, R. ; Neves, J. L. ; Todeschini, A. R. (2019). Duffy binding-like 1α adhesin from Plasmodium falciparum recognizes ABH histo-blood group saccharide in a type specific manner. Carbohydrate Polymers, v. 207, p. 266-275.
DOI: 10.1016/j.carbpol.2018.11.082
Lorenzon, E. N. ; Nobre, T. M. ; Caseli, L. ; Cilli, E. M. ; Da Hora, G. C. A. ; Soares, T. A. ; Oliveira, O. N. (2018) The “pre-assembled state” of magainin 2 lysine-linked dimer determines its enhanced antimicrobial activity. Colloids and Surfaces B: Biointerfaces, v. 167, p. 433-440.
DOI: 10.1016/j.colsurfb.2018.04.034
Paula, M.V. ; Barros, A.L. ; Wanderley, K.A. ; de Sá, G.F. ; Eberlin, M. ; Soares, T.A.; Alves-Jr. S. (2018) Metal Organic Frameworks for Selective Degradation of Amoxicillin in Biomedical Wastes. Journal of the Brazilian Chemical Society, v. 29, p. 2127-2136.
DOI: 10.21577/0103-5053.20180087
Da Silva, J. ; Dias, R. ; Da Hora, G. ; Soares, T.A. ; Meneghetti, M. (2018) Molecular Dynamics Simulations of Cetyltrimethylammonium Bromide (CTAB) Micelles and their Interactions with a Gold Surface in Aqueous Solution. Journal of the Brazilian Chemical Society, v. 29, p. 191-199.
DOI: 10.21577/0103-5053.20170130
Santos, D. E. S. ; Pol-Fachin, L. ; Lins, R. D. ; Soares, T. A. (2017) Polymyxin Binding to the Bacterial Outer Membrane Reveals Cation Displacement and Increasing Membrane Curvature in Susceptible but not in Resistant LPS Chemotypes. Journal of Chemical Information and Modeling, v. 57 (9), p. 2181–2193.
Casillas-Ituarte, N. N. ; Cruz, C. H. B. ; Lins, R. D. ; Dibartola, A. C. ; Howard, J. ; Liang, X. Höök, M. ; Viana, I. F. T. ; Sierra-Hernández, M. R. ; Lower, S. K. (2017) Amino acid polymorphisms in the fibronectin-binding repeats of fibronectin-binding protein A affect bond strength and fibronectin conformation. The Journal of Biological Chemistry, v. 292, p. 8797–8810.
Silva, L. N. ; Da Hora, G. C. A. ; Soares, T. A. ; Bojer, M. S. ; Ingmer, H. ; Macedo, A. J. ; Trentin, D. S. (2017) Myricetin protects Galleria mellonella against Staphylococcus aureus infection and inhibits multiple virulence factors. Scientific Reports, v. 7, p. 1-16.
DOI: 10.1038/s41598-017-02712-1
Soares, T. A. ; Vanni, S. ; Milano, G. ; Cascella, M. (2017) Toward Chemically Resolved Computer Simulations of Dynamics and Remodeling of Biological Membranes. Journal of Physical Chemistry Letters, v. 8, p. 3586-3594. (ACS VIDEO on our publication)
DOI: 10.1021/acs.jpclett.7b00493
Bozkurt, E. ; Soares, T. A. ; Rothlisberger, U. (2017) Can Biomimetic Zinc Compounds Assist a (3 + 2) Cycloaddition Reaction? A theoretical Perspective. Journal of Chemical Theory and Computation, v. 13, p. 6382-6390.
Freire, M. C. L. C. ; Pol-Fachin, L. ; Coêlho, D. F. ; Viana, I. F. T. ; Magalhães, T. ; Cordeiro, M. T. ; Fischer, N. ; Loeffler, F. F. ; Jaenisch, T. ; França, R. F. ; Marques, E. T. A. ; Lins, R. D. (2017) Mapping Putative B-Cell Zika Virus NS1 Epitopes Provides Molecular Basis for Anti-NS1 Antibody Discrimination between Zika and Dengue Viruses. American Chemical Society Omega, v. 2, p. 3913-3920.
Seo, S. ; Lee, D. W. ; Ahn, J. S. ; Cunha, K. ; Filippidi, E. ; Ju, S. W. ; Shin, E. ; Kim, Byeong-Su ; Levine, Z. A. ; Lins, R. D. ; Israelachvili, J. N. ; Waite, J. H. ; Valentine, M. T. ; Shea, J. E. ; Ahn, B. K. (2017) Significant Performance Enhancement of Polymer Resins by Bioinspired Dynamic Bonding. Advanced Materials, v. 00, p. 1703026.
Taylor, E. S. ; Pol-Fachin, L. ; Lins, R. D. ; Lower, S. K. (2017) Conformational stability of the epidermal growth factor (EGF) receptor as influenced by glycosylation, dimerization and EGF hormone binding. Proteins, v. 85, p. 561-570.
Colak, B. ; Da Silva, J. C. S. ; Soares, T. A. ; Gautrot, J. E. E. (2016) Impact of the Molecular Environment on Thiol–Ene Coupling For Biofunctionalization and Conjugation. Bioconjugate Chemistry, v. 27, p. 2111–2123.
DOI: 10.1021/acs.bioconjchem.6b00349
Da Hora, G. C. A. ; Archilha, N. L. ; Lopes, J. L. S. ; Muller, D. M. ; Cutinho, K. ; Itri, R. ; Soares, T.A. (2016) Membrane negative curvature induced by a hybrid peptide from pediocin PA-1 and plantaricin 149 as revealed by atomistic molecular dynamics simulations. Soft Matter, v. 12, p. 8884-8898.
Cornish, A. J. ; Ginovska, B. ; Thelen, A. ; da Silva, J. C. S. ; Soares, T. A. ; Raugei, S. ; Dupuis, M. ; Shaw, W. J. ; Hegg, E. L. (2016) Single-Amino Acid Modifications Reveal Additional Controls on the Proton Pathway of [FeFe]-Hydrogenase. Biochemistry. v. 55, p 3165-3173.
DOI: 10.1021/acs.biochem.5b01044
Pontes, F. J. S. ; Maia, R. T. ; Lima, M. C. P. ; Ayres, C. F. J. ; Soares, T. A. (2016) The Role of the Conformational Dynamics of Glutathione S-Transferase Epsilon Class on Insecticide Resistance. Journal of the Brazilian Chemical Society, v. 27, 1602-1615.
DOI: 10.5935/0103-5053.20160040
Lorezón, E. N. ; Riske, K. A. ; Troiano, G. F. ; Da Hora, G. C. A. ; Soares, T. A. ; Cilli, E. M. (2016) The Effect of dimerization on the mechanism of action of aurein 1.2. Biochimica et Biophysica Acta - Biomembranes, v. 1858, p. 1229-1238.
DOI: 10.1016/j.bbamem.2016.02.010
Viana, I. F. T. ; Nascimento, E. ; Craigo, J. ; Krieger, M. ; Mailliard, R. ; Dhalia, R. ; LINS, R. D. ; Marques, E. T. A. (2016) De Novo Design and Biophysical Characterization of an Affinity-Enhanced Protein Displaying the Structure of the Broadly Neutralizing HIV-1 2F5 Antibody Epitope. Biophysical Journal, v. 110, p. 346a.
DOI: 10.1016/j.bpj.2015.11.1860
Das, S. ; Lee, B. H. ; Linstadt, R. ; Cunha, K. ; Li, Y. ; Kaufman, Y. ; Levine, Z. A. ; Lipshutz, B. H. ; Lins, R. D. ; Shea, Joan-Emma ; Heeger, A. J. ; Ahn, K. (2016) . Molecularly smooth self-assembled monolayer for high-mobility polymer field-effect transistors. Nano Letters, v. 16(10), p. 6709–6715.
DOI: 10.1021/acs.nanolett.6b03860
Liu, J. ; Li, X. F. ; Gu, C. Y. ; Da Silva, J. C.S. ; Barros, A. L. ; Júnior, S. A. ; Li, B. H. ; Ren, F. ; Batten, S. R. ; Soares, T. A. (2015) A Combined Experimental and Computational Study of Novel Nanocage-based Metal-Organic Frameworks for Drug Delivery. Dalton Transactions, v. 44, p. 19370-19382.
Harper, B. ; Thomas, D. ; Chikkagoudar, S. ; Baker, N. ; Tang, K. ; Heredia-Langner, A. ; Lins, R. ; Harper, S. (2015) Comparative hazard analysis and toxicological modeling of diverse nanomaterials using the embryonic zebrafish (EZ) metric of toxicity. Journal of Nanoparticle Research, v. 17, p. 250.
DOI: 10.1007/s11051-015-3051-0
Xiong, Y. Q. ; Sharma-Kuinkel, B. K. ; Casillas-Ituarte, N. N. ; Fowler, V. G. ; Rude, T. ; Dibartola, A. C. ; Lins, R. D. ; Abdel-Hady, W. ; Lower, S. K. ; Bayer, A. S. (2015) Endovascular infections caused by methicillin-resistant Staphylococcus aureus are linked to clonal complex-specific alterations in binding and invasion domains of fibronectin-binding protein A as well as the occurrence of fnbB. Infection and Immunity, v. 83, p. 4772-4780.
Cunha, K. C. ; Rusu, V. H. ; Viana, I. F. T. ; Marques, E. T. A. ; Dhalia, R. ; Lins, R D. (2015) Assessing protein conformational sampling and structural stability via de novo design and molecular dynamics simulations. Biopolymers, v. 103, p. 351-361.
Dias, R. P. ; Da Hora, G. C.A. ; Ramstedt, M. ; Soares, T. A. (2014) Outer Membrane Remodeling: The Structural Dynamics and Electrostatics of Rough Lipopolysaccharide Chemotypes. Journal of Chemical Theory and Computation, v. 10, p. 2488-2497.
Dias, R. P. ; LI, L. ; Soares, T. A. ; Alexov, E. (2014) Modeling the electrostatic potential of asymmetric lipopolysaccharide membranes: The MEMPOT algorithm implemented in DelPhi. Journal of Computational Chemistry, v. 35, p. 1418-1429.
Carvalho, P. H. P. R. ; Correa, J. R. ; Guido, B. C. ; Gatto, C. C. ; De'Oliveira, H. C. B. ; Soares, T. A. ; Neto, B. A. D. (2014) Designed Benzothiadiazole Fluorophores for Selective Mitochondrial Imaging and Dynamics. Chemistry - A European Journal, v. 20, p. 15360-15374.
Liu, J. ; WU, J. ; Jia, Z. ; Chen, H. ; Daiguebonne, C.; Guillou, O. ; Sakiyamad, H. ; Soares, T. A. ; Ren, F. ; NG, S. W. ; Li, Q. (2014) Two isoreticular metal-organic frameworks with CdSO4-like topology: selective gas sorption and drug delivery. Dalton Transactions, v. 43, p. 17265-17273.
Nadvorny, D. ; Silva, J. B. P. ; Lins, R. D. (2014) Anionic form of Usnic Acid Promotes Lamellar to Non-lamellar transition in DPPC and DOPC Membranes. Journal of Physical Chemistry. B, v. 118, p. 3881-3886.
Fernandes, A. M. A. P. ; Fernandes, G. D. ; Barrera-Arellano, D. ; De Sá, G. F. ; Lins, R. D. ; Eberlin, M. N. ; Alberici, R. M. (2014) Desorption/ionization efficiencies of triacylglycerols and phospholipids via EASI-MS. Journal of Mass Spectrometry, v. 49, p. 335-341.
Pol-Fachin, Laercio ; Verli, Hugo ; Dias, R.L. (2014) Extension and validation of the GROMOS 53A6glyc parameter set for glycoproteins. Journal of Computational Chemistry, v. 35, p. 2087-2095.
Rusu, Victor H ; Baron, Riccardo ; Lins, R. D. (2014) PITOMBA: Parameter Interface for Oligosaccharide Molecules Based on Atoms. Journal of Chemical Theory and Computation, v. 10, p. 5068-5080.
Mota, A. A. R. ; Carvalho, P. H. P. R. ; Guido, B. C. ; Oliveira, H. C. B. ; Soares, T. A. ; Correa, J. R. ; Neto, B. A. D. (2014) Bioimaging, Cellular Uptake and Dynamics in Living Cells of a Lipophilic Fluorescent Benzothiadiazole at Low Temperature (4 °C). Chemical Science, v. 5, p. 3995-4003.
Ravi, H. K. ; Stach, M. ; Soares, T. A. ; Darbre, T. ; Reymond, J. L. ; Cascella, M. (2013). Electrostatics and Flexibility Drive Membrane Recognition and Early Penetration by Antimicrobial Peptide Dendrimer bH1. Chemical Communications, v. 49, p. 8821-8823.
Nascimento Jr., A. ; Pontes, F. J. S. ; Lins, R. D. ; Soares, T. A. (2013). Hydration, Ionic Valence and Cross-Linking Propensities of Cations Determine the Stability of Lipopolysaccharide Membranes. Chemical Communications, v. 50, p. 231-233.
Alvim, H. G. O. ; Fagg, E. L. ; de Oliveira, A. L. ; de Oliveira, H. C. B. ; Freitas, S. M. ; Xavier, M. A. E. ; Soares, T. A. ; Gomes, A. F. ; Gozzo, F. C. ; Silva, W. ; Neto, B. A. D. (2013) Probing Deep into the Interaction of a Fluorescent Chalcone Derivative and Bovine Serum Albumin (BSA): An Experimental and Computational Study. Organic and Biomolecular Chemistry, v. 11, p. 4764-4777.
Viana, I. F. T. ; Dhalia, R. ; Krieger, M. ; Marques, E. T. A. ; Lins, R. D. (2013) Influence Of Scaffold Stability And Electrostatics On Top7-Based Engineered Helical HIV-1 Epitopes. Lecture Notes In Bioinformatics, v. 8213, p. 94-103.
DOI: 10.1007/978-3-319-02624-4_9
Ravi, H. K. ; Stach, M. ; Soares, T. A. ; Darbre, T. ; Reymond, Jean-Louis; Cascella, M. (2013) Electrostatics and Flexibility Drive Membrane Recognition and Early Penetration by Antimicrobial Peptide Dendrimer bH1. Chemical Communications. v. 49, p. 8821-8823, 2013.
Viana, I. F. T. ; Soares, T. A. ; Lima, L. F. O. ; Marques, E. T. A. ; Krieger, M. ; Dhalia, R. ; Lins, R. D. (2013) De Novo Design of Immunoreactive Conformation-specific HIV-1 Epitopes Based on Top7 Scaffold. Royal Society of Chemistry Advances, v. 3, p. 11790-11800.
Soares, T. A. ; Oliveira, V. S. ; Pimenteira, C. ; Da Silva-Alves, D. C. B. ; Leal, L. L. L. ; Neves-Filho, R. A. W. ; Navarro, D. M. A. F. ; Santos, G. K. N. ; Dutra, K. A. ; Dos Anjos, J. V. (2013) The enzyme 3-hydroxykynurenine transaminase as potential target for 1,2,4-oxadiazoles with larvicide activity against the dengue vector Aedes aegypti. Bioorganic and Medicinal Chemistry, v. 21, p. 6996-7003.
DOI: 10.1016/j.bmc.2013.09.020
De Carvalho, R. V. ; Lopez-Ferrer, D. ; Guimarães, K. S. ; Lins, R. D. (2013) IMS Peptider, a computational peptide collision cross-section area calculator based on a novel molecular dynamics simulation protocol. Journal of Computational Chemistry, v. 34, p. 1707–1718.
Pol-Fachin, L. ; Rusu, V. H. ; Verli, H. ; Lins, R. D. (2012) GROMOS 53A6 , an Improved GROMOS Force Field for Hexopyranose-Based Carbohydrates. Journal of Chemical Theory and Computation, v. 8, p. 4681-4690.
Kirschner, K. N. ; Lins, R. D. ; Maass, A. ; Soares, T. A. (2012) A GLYCAM-based force field for simulations of lipopolysaccharide membranes: parametrization and validation. Journal of Chemical Theory and Computation, v. 8, p. 4719–4731.
Vasconcelos I.B. ; Silva, T. ; Milito, G. ; Soares, T. A. ; Rodrigues, M. O. ; Costa Jr, N. B. ; Freire, R. O. ; Alves Jr, S. (2012) Cytotoxicity and slow release of the anti-cancer drug doxorubicin from ZIF-8. Royal Society of Chemistry Advances, v. 2, p. 9437-9442.
Pontes, F. J. S. ; Rusu, V. H. ; Soares, T. A. ; Lins, R. D. (2012) The effect of temperature, cations and number of acyl chains on the lamellar to non-lamellar transition in lipid-A membranes: a microscopic view. Journal of Chemical Theory and Computation, v. 8, p. 3830–3838.
de Paula, M. V. ; Rodrigues, M. O. ; Wanderley, K. A. ; Vasconcelos, I. B. ; Alves Jr, S. ; Soares, T. A. (2012) Metal Organic Frameworks for Drug Delivery and Environmental Remediation: A Molecular Docking Approach. Inter. Journal Quantum Chemistry, v. 112, p. 3346-3355.
Gomes, D. E. B. ; Lins, R. D. ; Pascutti, P. G. ; Lei, C. ; Soares, T. A. (2011) Conformational Variability of Organophosphorous Hydrolase upon Soman and Paraoxon Binding, Journal of Physical Chemistry B, v. 115, p. 15389-15398.
Lower et al., (2011) Polymorphisms in fibronectin binding protein A of Staphylococcus aureus are associated with infection of cardiovascular devices, Proceedings of the National Academy of Sciences, v. 108, p. 18372-18377.
França, E. F. ; Freitas, L. C. G. ; Lins, R. D. (2011) Chitosan molecular structure as a function of N-acetylation, Biopolymers, v. 95, p. 448-460.
DOI: 10.1002/bip.21602
Lins, R. D. ; Devanathan, R. ; Dupuis, M. (2011) Modeling the Nanophase Structural Dynamics of Phenylated Sulfonated Poly Ether Ether Ketone Ketone (Ph-SPEEKK) Membranes as a Function of Hydration, Journal of Physical Chemistry B, v. 115, p. 1817-1824.
Gomes, D. E. B. ; Lins, R. D. ; Pascutti, P. G. ; Lei, C. ; Soares, T. A. (2010) The Role of nonbonded interactions in the conformational dynamics of organophosphorous hydrolase adsorbed onto functionalized sílica surfaces, Journal of Physical Chemistry B, v. 114, p. 513-540.
Ferreira, R. ; Lai, C. ; Lins, R. D. (2010) Prebiotic chemical kinetics imprint on positional codon usage. Journal of Brazilian Chemical Society, v. 21, p. 1117-1120.
DOI: 10.1590/S0103-50532010000600022
Soares, T. A. ; Boschek, C. B. ; Apiyo, D. ; Baird, C. ; Straatsma, T. P. (2010) Molecular basis of the structural stability of a Top7-based scaffold at extreme pH and temperature conditions.Journal of Molecular Graphics and Modelling, v. 28, p. 755-765.
DOI: 10.1016/j.jmgm.2010.01.013
Boily, J-F. ; Lins, R. D. (2009) Electrostatic cooperativity of hydroxyl gropus at metal oxide surfaces, Journal of Physical Chemistry C, v. 113, p. 16568-16570.
Chen, L. T. L. ; Yao, Q. ; Soares, T. A. ; Squier, T. C. ; Bigelow, D. J. (2009) Phospholamban Modulates the Functional Coupling between Nucleotide Domains in Ca-ATPase Oligomeric Complexes in Cardiac Sarcoplasmic Reticulum. Biochemistry, v. 48, p. 2411-2421.
Oliveira, O. V. ; Freitas, L. C. G. ; Straatsma, T. P. ; Lins, R. D. (2009) Interaction between the CBM of Cel9A from Thermobifida fusca and cellulose fibers, Journal of Molecular Recognition, v. 22, p. 38-45.
Straatsma, T. P. ; Soares, T. A. (2009) Characterization of the outer membrane protein OprF of Pseudomonas aeruginosa in a lipopolysaccharide membrane by computer simulation. Proteins, v. 74, p. 475-488.
DOI: 10.1002/prot.22165
Apiyo, D. O. ; Soares, T. A. ; Engelmann, H. E. ; Pefaur, N. B. ; Straatsma, T. P. ; Baird, C. L. (2009) Engineering an ultra-stable affinity reagent based on Top7. Protein Engineering, Design and Selection, v. 22, p. 325-332.
Franca E.F. ; Lins R.D. ; Freitas L.C.G. ; Straatsma T.P. (2008) Characterization of the molecular structure and chitin and chitosan molecules in aqueous solution, Journal of Chemical Theory and Computation, v. 4, p. 2141-2149.
Lower B.H.; Lins R.D. ; Oestreicher Z. ; Straatsma T.P. ; Hochella Jr. M.F. ; Shi L. ; Lower S.K. (2008) In vitro evolution of a peptide with a hematite binding peptide motif that may constitute a natural metal-oxide binding archetype, Environmental Science and Technology, v. 42, p. 3821-3827.
Soares, T. A. ; Straatsma, T. P. (2008) Assessment of the convergence of molecular dynamics simulations of lipopolysaccharide membranes. Molecular Simulation, v. 34, p. 295-307.
DOI: 10.1080/08927020701829880
Lei, C. ; Soares, T. A. ; Shin, Y. ; Liu, J. ; Ackerman, E.J. (2008) Enzyme specific activity in functionalized nanoporous supports. Nanotechnology, v. 19, p. 125102.
DOI: 10.1088/0957-4484/19/12/125102
Gomes D.E.B. ; Lins R.D. ; Pascutti P.G. ; Straatsma T.P. ; Soares, T.A. (2008) Molecular Models to Emulate Confinement Effects on the Internal Dynamics of Organophosphorous Hydrolase, Lecture Notes in Bioinformatics, v. 5167, p. 68-78.
DOI: 10.1007/978-3-540-85557-6_7
Lins R.D. ; Vorpagel E.R. ; Guglielmi M. ; Straatsma T.P. (2008) Computer Simulation of Uranyl Uptake by the Rough Lipopolysaccharide Membrane of Pseudomonas aeruginosa, Biomacromolecules, v. 9, p. 29-35.
Peterson E.S. ; Williams L. ; Stephan E.G. ; Rose S. ; Corrigan A. ; Lai C. ; Lins R.D. ; Critchlow T. ; Straatsma T.P. ; Soares T.A. ; Scarberry R. (2008) Northwest Trajectory Analysis Capability: A Platform for Enhancing Computational Biophysics Analysis, In Proceedings of the 2008 International Conference on Bioinformatics and Computational Biology, BIOCOMP 2008, pp. 558-562. CSREA Press, Bogart, GA
Soares T.A., Straatsma T.P., and Lins R.D. (2008) Influence of the B-band O-antigen chain in the Structure and Electrostatics of the Lipopolysaccharide Membrane of Pseudomonas aeruginosa, Journal of Brazilian Chemical Society, v. 19, p. 312-320 (invited contribution in honor to the 80th birthday of Prof. R. C. Ferreira). Invited peer-review contribution to special issue dedicated to the 80th Birthday of Prof. Ricardo Ferreira
DOI: 10.1590/S0103-50532008000200018
Pereira C.S. ; Moura A.F. ; Freitas L.C.G. ; Lins R.D. (2007) Revisiting the Internal Conformational Dynamics and Solvation Properties of Cyclodextrins, Journal of Brazilian Chemical Society, v.18, p. 951-961.
DOI: 10.1590/S0103-50532007000500012
Soares, T. A. ; Osman, M.A. ; Straatsma, T.P. (2007) Molecular Dynamics of Organophosphorous Hydrolases Bound to the Nerve Agent Soman. Journal of Chemical Theory and Computation, v. 3, p. 1569-1579.
Trzesniak, D. ; Lins R.D. ; van Gunsteren W.F. (2006) A Protein under Pressure: Molecular Dynamics Simulation of the Arc Repressor, Proteins: Structure, Function and Bioinformatics, v. 65, p. 136-144.
Lins R.D. ; Roethlisberger U. (2006) Influence of Long-range Electrostatic Treatments on the Folding of the N-terminal H4 Histone Tail Peptide, Journal of Chemical Theory and Computation, v. 2, p. 246-250.
Lins, R.D.; Ferreira, R. (2006) The Stability of Right- and Left-Handed α-Helices as a Function of Monomer Chirality, Quimica Nova, v. 29, p. 997-998.
DOI: 10.1590/S0100-40422006000500020
von Lilienfeld, O.A.; Lins, R.D. ; Röthlisberger U. (2005) General Rational Compound Design from Grand-Canonical Emsemble Density Functional Theory, Phys. Lett. Rev., 95: 153002. (Featured the cover of Physical Review Letters volume 95 (15), 2005, issue of October 7; Republished in the Virtual Journal of Biological Physics Research, volume 10 (8), a journal from the American Institute of Physics and the American Physical Society.).
DOI: 10.1103/PhysRevLett.95.153002
Lins, R.D. ; Hünenberger, P.H. (2005) Engineering of a New GROMOS Force Field for Hexopyranoses, Journal of Computational Chemistry, v. 26, p. 1400-1412.
Soares, T.A. ; Hünenberger, P.H. ; Kastenholtz, M. ; Krautler, V. ; Lenz T. ; Lins, R.D. ; Oostenbrink, C. ; van Gunsteren, WF. (2005) Development of a Consistent Nucleic Acid Parameter Set for the GROMOS Force Field, Journal of Computational Chemistry, v. 26, p. 725-737.
Oostenbrink, C. ; Soares, T. A. ; Vegt, N. F. A. ; van Gunsteren, W.F. (2005) Validation of the 53A6 GROMOS force field. European Biophysics Journal, v. 34, p. 273-284.
DOI: 10.1007/s00249-004-0448-6
Soares, T.A. ; Daura, X.; Oostenbrink, C. ; Smith, L. J. ; van Gunsteren, W. F. (2004). Validation of the GROMOS force-field parameter set 45A3 against nuclear magnetic resonance data of hen egg lysozyme. Journal of Biomolecular NMR, v. 30, p. 407-422, 2004.
DOI: 10.1007/s10858-004-5430-1
Lins, R.D. ; Pereira, C.S. ; Hunenberger P.H. (2004) Protein-Trehalose Interactions in Aqueous Solution. Proteins, v. 55, p. 177-186.
Pereira, C.S. ; Lins, R.D ; Chandrasekhar, I. ; Freitas, L.C.G. ; Hunenberger, P.H. (2004) Interaction of the Disaccharide Trehalose with a Phospholipid Bylayer: A Molecular Dynamics Study. Biophysical Journal, v. 86, p. 2273-2285.
DOI: 10.1016/S0006-3495(04)74285-X
Adesokan, A.A. ; Roberts, V.A. ; Lee, K.W. ; Lins, R.D. ; Briggs, JM. (2004) Prediction of HIV-1 Integrase/Viral DNA Interactions in the Catalytic Domain by Fast Molecular Docking. Journal of Medicinal Chemistry, v. 47(4), p. 821-828.
Soares, T. ; Christen, M. ; Hu, K ; van Gunsteren, W.F. (2004) Alpha- and beta-polypeptides show a different stability of helical secondary structure. Tetrahedron. v. 60, p. 7775 - 7780.
DOI: 10.1016/j.tet.2004.06.062
Soares, T. A. ; Ferreira, R. (2004) Applications of the Poisson-Boltzmann equation to the calculation of pH-dependent properties in proteins. Química Nova. v. 27, p. 640 - 647.
DOI: 10.1590/S0100-40422004000400019
Chandrasekar, I. ; Kastenholtz, M. ; Lins, R.D. ; Oostenbrink, C.; Schuler, L.D.; Tieleman P.D. ; Hünenberger, P.H. ; van Gunsteren W.F. (2003) A Consistent Potential Energy Parameters Set for Lipids. Dipalmitoylphosphatidylcholine as benckmark of the GROMOS96 45A3 force field. European Biophysics Journal, v. 32, p. 67-77.
DOI: 10.1007/s00249-002-0269-4
Mustata, G.I. ; Soares, T. A.; Briggs, J.M. (2003) Molecular dynamics studies of alanine racemase: A structural model for drug design. Biopolymers. v. 70, p.186 - 200.
Soares, T.A. ; Lins, R.D. ; Straatsma, T.P. ; Briggs, J.M. (2002) Internal dynamics and ionization states of the macrophage migration inhibitory factor: Comparison between wild-type and mutant forms. Biopolymers, v. 65, p. 313-323.
Lins, R.D. ; Straatsma, T.P. (2001) Computer Simulation of the Rough Lipopolysaccharide Membrane of Pseudomonas aeruginosa. Biophysical Journal, v. 81, p. 1037-1046.
DOI: 10.1016/S0006-3495(01)75761-X
van Gunsteren, W. F. ; Soares, T. A. et al. (2001) Molecular dynamics simulation of biomolecular systems. Chimia. v. 55, p. 856 - 860.
Soares, T. A. ; Straatsma, T.P. ; Miller, J. H. (2001) Revisiting the structural flexibility of the complex p21(ras)-GTP: The catalytic conformation of the molecular switch II. Proteins. v. 45, p. 297 - 312.
Hünenberger, P.H. ; Borjesson U. ; Lins, R.D. (2001) Electrostatic interactions in biomolecular systems. Chimia, v. 55, p. 861-866
Soares, T. A. (2001) Women in science and technology: Restricted success. Química Nova. v. 24, p. 281 - 285.
DOI: 10.1590/S0100-40422001000200020
Carlson, H.A. ; Masukawa, K.M. ; Rubins, K. ; Bushman, F.D. ; Jorgensen, W.L. ; Lins, R.D. ; Briggs, J.M. ; McCammon, J.A. (2000) Developing a Dynamic Pharmacophore Model for the HIV-1. Journal of Medicinal Chemistry, v. 43, p. 2100-2114.
Lins, R.D. ; Adesokan, A.A. ; Soares, T.A ; Briggs, J.M. (2000) Investigations On Human Immunodeficiency Virus Type-1 Integrase/DNA Binding Interactions via Molecular Dynamics and Electrostatics Calculations.Pharmacology and Therapeutics, v. 85, p. 123-131.
DOI: 10.1016/S0163-7258(99)00059-5
Soares, T. A. ; Goodsell, D. S., Ferreira, R. ; Olson, A. J. ; Briggs, J.M. (2000) Ionization state and molecular docking studies for the macrophage migration inhibitory factor: the role of lysine 32 in the catalytic mechanism. Journal of Molecular Recognition, v. 13, p. 146 - 156.
DOI: 10.1002/1099-1352(200005/06)13:3<146::AID-JMR497>3.0.CO;2-4
Soares, T. A.; Goodsell, D. S. ; Briggs, J.M. ; Ferreira, R. ; Olson, A. J. (1999) Docking of 4-oxalocrotonate tautomerase substrates: Implications for the catalytic mechanism. Biopolymers, v. 50, p. 319 - 328.
DOI: 10.1002/(SICI)1097-0282(199909)50:3<319::AID-BIP7>3.0.CO;2-8
Lins, R.D. ; Briggs, J.M. ; Straatsma, T.P. ; Carlson H.A. ; Greenwald J. ; Choe S. ; McCammon, J.A. (1999) Molecular Dynamics Studies on the HIV-1 Integrase Catalytic Core Domain. Biophysical Journal, v. 76, p. 2999-3011.
DOI: 10.1016/S0006-3495(99)77453-9
Lins, R.D. ; Soares, T.A. ; Ferreira, R. ; Longo R. (1999) Solvent Access to Aspartyl and Succinimidyl residues in the Amyloid 1-28 beta peptide. Zeitschrift für Naturforschung, v. 54c, p. 264-270.
Weber, W. ; Demirdjan, H. ; Lins, R.D. ; Briggs, J.M. ; Ferreira R. ; McCammon, J.A. (1998) Brownian and Essential Dynamics Studies of the HIV-1 Integrase Catalytic Core Domain. Journal of Biomolecular Structure & Dynamics, v. 16, p. 733-745.
DOI: 10.1080/07391102.1998.10508285
Lins, R.D. ; Soares, T.A. ; Ferreira R. (1998) Unusual Kinetic Pathway for the Prebiotic Oligomerization of Ribonucleic Acids Explains the Monochirality of the Polyribotides. Anais da Academia Brasileira de Ciências, v. 70, p. 423-428.
Soares; T.A. ; Lins, R.D. ; Longo, R. ; Garratt, R. ; Ferreira, R. (1997) Plural Origins of Molecular Homochirality in our Biota, PartII. The Relative Stabilities of Homochiral and Mixed Oligoribotides and Peptides. Zeitschrift für Naturforschung, v. 52c, p. 89-96.
Lins, R.D. ; Soares, T.A. ; Ferreira, R. (1996) Plural Origins of Molecular Homochirality in our Biota. Zeitschrift für Naturforschung, v. 51c, p.70-74.
Soares, T.A. 1996. Introduction to the study of the ribozymes. Brazilian Society of Genetics Publisher. São Paulo, Brazil. 200 p. (BOOK)
Soares, T.A. ; Lins R.D. (1995) Ribozymes - not every enzyme is a protein. Quimica Nova,
v. 18, p. 375-378. http://quimicanova.sbq.org.br/imagebank/pdf/Vol18No4_375_v18_n4_09.pdf
SOARES, T. A. ; Garratt, R. ; Ferreira, R. . Estudos Por Simulacao Computacional de Alfa-Helices Formadas Por Aminoacidos D/L.. Anais da Academia Brasileira de Ciências (Impresso), Brasil, v. 66, n.3, p. 393-393, 1994.